Reviewing February Goals
✔️ Set up RNAseq DGE analysis pipeline for when we get the cod RNAseq data back.
⏳ Connect with Laura to get details on the cod project’s experimental setup/implementation
✔️ Start and make progress on a lit review for the cod project/manuscript
⏸️ Either send cod samples for methylation sequencing or, if we decide to do extractions in-house, establish a reasonable timeline for extraction, DNA QC, and sequencing.
✔️ Make progress on E5 gene expression work and generate a deliverable (either for lab meeting or molecular group meeting)
✔️ Choose objective/hypotheses and plan oyster experiment
Back-burner goals
❌ Look into several grants/funding sources that I may want to apply for over the next year or so (GRFP, Fulbright, etc.)
This month was quite busy, and I think I did a decent job of meeting my goals. I’ve QC’d the cod RNAseq data and have a basic DGE analysis pipeline set up to run it through once I’m back in office. I haven’t connected with Laura about the experimental methods, but Steven said he could get me that info himself, since he was directly involved, and I’ve outlined a place in the cod manuscript for him to provide methods details. I have a preliminary lit review for both the cod project and the oyster project going, and have implemented a new spreadsheet system to help me keep better track of what information I learn where. I haven’t made any progress with the cod methylation, but that’s intentional – we decided to wait until we took a look at the RNAseq data to send out samples for WGBS. I troubleshooted several issues with getting the right E5 deep dive transcriptomes, so we’re in a good place to start with co-expression analysis (and Zach is taking point on that right now, since he has some sample pipelines from Ariana). Finally, I had a big push during the last two weeks of February to develop a plan for the oyster experiment I want to run, and I think we’re getting there! The big picture is set, now I just need to figure out some details (e.g. how high should the stress temp be, what equipment do we need for monitoring, etc.)
We also started pubathon this month, so I’m expecting the next month to have slightly more focus on writing up the things I’m working on.
March Goals
I’m out for a little over a week this month (March 6-15), so I have a more limited set of goals
Write a draft proposal for the oyster project
Finish DGE analysis for cod project
Write full methods section draft (both experimental and analysis sections) for the cod manuscript (part of pubathon)
Start a planning document for the oyster project in the same style as Ariana showed us during lab meeting (see daily post)
Back-burner goals (again)
- Look into several grants/funding sources that I may want to apply for over the next year or so (GRFP, Fulbright, etc.)